[RASMB] SAXS versus Sed. Vel.

[Mullins, Dyche]

Dear All,

We have been looking at nucleotide-dependent conformational changes in several proteins, using both sedimentation velocity and small-angle X-ray scattering (SAXS). Interestingly, we get different results for the magnitude of the nucleotide-induced conformational change and, systematically, the AUC measurement suggests a larger change than the SAXS measurement. For one protein, for example, SAXS predicts sedimentation coefficients of 2.99 and 3.07 for nucleotide-free and nucleotide-bound forms (and for what it’s worth, these values match calculations based on crystal structures of the apo and ADP forms of the protein). By AUC, however, we measure values of 3.00 and 3.15. For the other protein the situations is almost exactly the same: AUC reports a change in S value almost twice that computed from SAXS. 

I suppose pressure might cause additional conformational changes. What else are we missing? 

Thank you,
Dyche Mullins
UCSF